Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States.
J Am Chem Soc. 2022 Apr 13;144(14):6361-6372. doi: 10.1021/jacs.2c00435. Epub 2022 Mar 30.
Guanine (G)-oxidation to 8-oxo-7,8-dihydroguanine (OG) by reactive oxygen species in genomic DNA has been implicated with various human diseases. G-quadruplex (G4)-forming sequences in gene promoters are highly susceptible to G-oxidation, which can subsequently cause gene activation. However, the underlying G4 structural changes that result from OG modifications remain poorly understood. Herein, we investigate the effect of G-oxidation on the gene promoter G4. For the first time, we show that OG can induce a G-vacancy-containing G4 (vG4), which can be filled in and stabilized by guanine metabolites and derivatives. We determined the NMR solution structure of the cGMP-fill-in oxidized promoter vG4. This is the first complex structure of an OG-induced vG4 from a human gene promoter sequence with a filled-in guanine metabolite. The high-resolution structure elucidates the structural features of the specific 5'-end cGMP-fill-in for the OG-induced vG4. Interestingly, the OG is removed from the G-core and becomes part of the 3'-end capping structure. A series of guanine metabolites and derivatives are evaluated for fill-in activity to the oxidation-induced vG4. Significantly, cellular guanine metabolites, such as cGMP and GTP, can bind and stabilize the OG-induced vG4, suggesting their potential regulatory role in response to oxidative damage in physiological and pathological processes. Our work thus provides exciting insights into how oxidative damage and cellular metabolites may work together through a G4-based epigenetic feature for gene regulation. Furthermore, the NMR structure can guide the rational design of small-molecule inhibitors that specifically target the oxidation-induced vG4s.
活性氧物种使基因组 DNA 中的鸟嘌呤（G）氧化为 8-氧代-7,8-二氢鸟嘌呤（OG），这与多种人类疾病有关。基因启动子中形成 G-四链体（G4）的序列极易受到 G-氧化的影响，从而导致基因激活。然而，OG 修饰导致的潜在 G4 结构变化仍知之甚少。在此，我们研究了 G-氧化对基因启动子 G4 的影响。我们首次表明，OG 可以诱导含有 G-空位的 G4（vG4），而鸟嘌呤代谢物和衍生物可以填充和稳定 vG4。我们确定了 cGMP 填充氧化启动子 vG4 的 NMR 溶液结构。这是第一个来自人类基因启动子序列的 OG 诱导 vG4 的复合物结构，其中包含填充的鸟嘌呤代谢物。高分辨率结构阐明了 OG 诱导 vG4 的特定 5'-端 cGMP 填充的结构特征。有趣的是，OG 从 G-核心中去除，并成为 3'-端封端结构的一部分。一系列鸟嘌呤代谢物和衍生物被评估用于填充氧化诱导的 vG4。值得注意的是，细胞鸟嘌呤代谢物，如 cGMP 和 GTP，可以结合并稳定 OG 诱导的 vG4，表明它们在生理和病理过程中对氧化损伤的潜在调节作用。因此，我们的工作为了解氧化损伤和细胞代谢物如何通过基于 G4 的表观遗传特征协同作用来调节基因提供了令人兴奋的见解。此外，NMR 结构可以指导针对氧化诱导的 vG4 的小分子抑制剂的合理设计。
